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Comparative Study
. 2005 Dec 30;6 Suppl 1(Suppl 1):S7.
doi: 10.1186/1471-2156-6-S1-S7.

Comparison of the power between microsatellite and single-nucleotide polymorphism markers for linkage and linkage disequilibrium mapping of an electrophysiological phenotype

Hsiu-Fen Lin  1 , Suh-Hang Hank Juo, Rong Cheng
Affiliations
Comparative Study

Comparison of the power between microsatellite and single-nucleotide polymorphism markers for linkage and linkage disequilibrium mapping of an electrophysiological phenotype

Hsiu-Fen Lin et al. BMC Genet. .

Abstract

We performed linkage and linkage disequilibrium (LD) mapping analyses to compare the power between microsatellite and single nucleotide polymorphism (SNP) markers. Chromosome-wide analyses were performed for a quantitative electrophysiological phenotype, ttth1, on chromosome 7. Multipoint analysis of microsatellite markers using the variance component (VC) method showed the highest LOD score of 4.20 at 162 cM, near D7S509 (163.7 cM). Two-point analysis of SNPs using the VC method yielded the highest LOD score of 3.98 in the Illumina SNP data and 3.45 in the Affymetrix SNP data around 152-153 cM. In family-based single SNP and SNP haplotype LD analysis, we identified seven SNPs associated with ttth1. We searched for any potential candidate genes in the location of the seven SNPs. The SNPs rs1476640 and rs768055 are located in the FLJ40852 gene (a hypothetical protein), and SNP rs1859646 is located in the TAS2R5 gene (a taste receptor). The other four SNPs are not located in any known or annotated genes. We found the high density SNP scan to be superior to microsatellites because it is effective in downstream fine mapping due to a better defined linkage region. Our study proves the utility of high density SNP in genome-wide mapping studies.

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Figures

Figure 1
Figure 1
Microsatellite multipoint VC analysis for ttth1 (chromosome 7). Microsatellite marker multipoint VC analyses for quantitative trait ttth1 on chromosome 7.
Figure 2
Figure 2
Age- and sex-adjusted SNP two-point VC analysis for ttth1 on chromosome 7. Age- and sex-adjusted SNP two-point VC analyses for quantitative trait ttth1 on chromosome 7.
See this image and copyright information in PMC

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